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. 2020 Oct 27;10(11):257. doi: 10.3390/life10110257

Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans

Hisayuki Komaki 1,*, Tomohiko Tamura 1
PMCID: PMC7692728  PMID: 33120960

Abstract

(1) Background: Phytohabitans is a recently established genus belonging to rare actinomycetes. It has been unclear if its members have the capacity to synthesize diverse secondary metabolites. Polyketide and nonribosomal peptide compounds are major secondary metabolites in actinomycetes and expected as a potential source for novel pharmaceuticals. (2) Methods: Whole genomes of Phytohabitans flavus NBRC 107702T, Phytohabitans rumicis NBRC 108638T, Phytohabitans houttuyneae NBRC 108639T, and Phytohabitans suffuscus NBRC 105367T were sequenced by PacBio. Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters were bioinformatically analyzed in the genome sequences. (3) Results: These four strains harbored 10, 14, 18 and 14 PKS and NRPS gene clusters, respectively. Most of the gene clusters were annotated to synthesis unknown chemistries. (4) Conclusions: Members of the genus Phytohabitans are a possible source for novel and diverse polyketides and nonribosomal peptides.

Keywords: actinomycete, genome, Phytohabitans, polyketide, nonribosomal peptide

1. Introduction

The discovery of new bioactive secondary metabolites remains one of the most important tasks for current pharmaceutical developments. Actinomycetes are well known as a potential source of diverse secondary metabolites. Numerous numbers of actinomycete strains have been isolated from soils and contributed to the discovery of useful bioactive compounds. However, it is nowadays becoming difficult to find novel compounds from soil-derived strains. That is because the majority of actinomycetal strains isolated from soil samples belong to the genus Streptomyces [1] and intensive exploration of Streptomyces strains is leading to frequent re-discovery of already reported compounds [2]. Consequently, attention has shifted from Streptomyces to the rare actinomycetes, especially new genera, because they are not extensively examined for the aim. New ecological niches are drawing attention as sources of new actinomycetes. The microbial flora in plant matter was reported to be different from that in soil samples and that the majority of species in such samples were rare actinomycetes [3].

Post-genomic studies for actinomycetes revealed that each actinomycete harbors in general diverse secondary metabolite-biosynthetic gene clusters (smBGCs) even if the strain had been reported to produce only few compounds [4]. This led to an approach based on analyzing smBGCs in whole genomes, called genome-mining, to search new natural products, resulting in effective isolation of new secondary metabolites [5]. Major smBGCs in actinomycetes are associated with polyketide synthase (PKS) and/or nonribosomal peptide synthase (NRPS) pathways [4,6]. Polyketide and nonribosomal peptide compounds are structurally and pharmacologically diverse and expected as a source for pharmaceutical seeds. Type-I PKSs and NRPS are large enzymes, composed of multiple catalytic domains organized into modules. Each module carries out a cycle of chain elongation, and typically contains at least three domains: a ketosynthase (KS) domain, an acyltransferase (AT) domain and an acyl carrier protein (ACP) in a PKS module; a condensation (C) domain, an adenylation (A) domain, and a thiolation (T) domain in an NRPS module. Optional domains are often present in modules to modify elongating chains chemically. The chains are synthesized from simple building blocks, such as acyl-CoA and amino-acid units by PKS and NRPS gene clusters, respectively, based on the collinearity rule of assembly-line enzymology. Therefore, chemical structures of synthesized polyketide and/or peptides can be predicted from the domain organization of these gene clusters [7].

The genus Phytohabitans was recently proposed as a new genus of the family Micromonosporaceae [8] and included four species, Phytohabitans flavus, Phytohabitans rumicis, Phytohabitans houttuyneae, and Phytohabitans suffuscus, all of which were isolated from the root tissues of plants [9], when we began this study. No genome sequences are published for this genus. Although a new meroterpenoid habiterpenol was discovered from a strain of Phytohabitans suffuscus [10], no polyketide and nonribosomal peptide compounds have been reported from members of the genus yet. To elucidate the capacity to synthesize polyketide and nonribosomal peptide compounds, we conducted whole genome-sequencing for type strains of these species and bioinformatically analyzed PKS and NRPS gene clusters.

2. Materials and Methods

2.1. Whole Genome Sequencing

P. flavus NBRC 107702T, P. rumicis NBRC 108638T, P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T were distributed from the NBRC Couture Collection. Their genomic DNA was prepared and whole genome de novo sequencing was performed by Macrogen Korea, employing the SMRT strategy using PacBio RSII with SMRT cell 8Pac V3 and the DNA Polymerase Binding Kit P6, according to the procedure reported previously [11]. The reads of each strain were assembled using Canu (version 1.4). Their genome sequences were assembled into one, three, five and one scaffolds,, respectively, and have been published under the accession numbers as follows: P. flavus NBRC 107702T, AP022870; P. rumicis NBRC 108638T, BLPG01000001–BLPG0100003; P. houttuyneae NBRC 108639T, BLPF01000001–BLPF0100005; P. suffuscus NBRC 105367T, AP022871.

2.2. Analysis of PKS and NRPS Gene Clusters

PKS and NRPS gene clusters in the genomes were surveyed using antiSMASH and then manually analyzed in the same manner of our previous reports [12,13,14]. Subtypes of C domains were characterized with NaPDoS (http://napdos.ucsd.edu/run_analysis.html) [12]. Substrates of A domains predicted by antiSMASH were also checked using NRPSsp (http://www.nrpssp.com/execute.php) [13] and/or by the specificity-conferring codes [14]. If the same substrates are predicted between antiSMASH and NRPSsp or the selectivity-conferring codes showed >90% identity to those for the predicted amino acids, the substrates are shown in the tables. If not, the amino acids predicted by antiSMASH are shown in italics in tables. Based on the substrates, domain organization, module number, and the collinearity rule of the assembly-line enzymology [7], we predicted the chemical structures of the peptides and polyketide chains synthesized by NRPS and PKS gene clusters [15,16,17]. Norine (https://bioinfo.cristal.univ-lille.fr/norine/form2.jsp) [18] was used to search similar nonribosomal peptides.

2.3. LC-MS Analysis of Culture Extracts

P. flavus NBRC 107702T, P. rumicis NBRC 108638T, P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T were cultured on double diluted TSA (20 g/L Bacto Tryptic Soy Agar, 7.5 g/L agar) and double diluted ISP-2 agar (2 g/L glucose, 5 g/L malt extract, 2 g/L yeast extract, 17 g/L agar) plates for 2 to 3 weeks at 28 °C. They were extracted by 3 times volume of ethanol at 4 °C overnight. One microliter of each supernatant was analyzed using an UHPLC system coupled with a mass spectrometer (LC-MS) (UltiMate 3000 UHPLC coupled with Q Exactive, Thermo Fisher Scientific K.K., Tokyo, Japan). Acquity UPLC BEH C18 1.7 μm (2.1 × 50 mm) (Nihon Waters K.K., Tokyo, Japan) was used as a reverse phase column for separation in the system. Water (solvent A) and acetonitrile (solvent B), both containing 0.1% (v/v) formic acid, were used as the mobile phase in the following linear gradient program: 5% B for 0.5 min, 5% B to 85% B in 5 min, 85% B to 100% B in 0.5min, 100% B for 2 min. The flow rate was set to 0.6 mL/min and the column oven temperature was set at 40 °C. Compounds in the eluate were detected in the electrospray ionization positive-ion mode with a spray voltage at 3.5 kV and a capillary temperature at 300 °C. Nitrogen sheath gas and auxiliary gas were set at 50 and 15 arbitrary units, respectively. A full MS scan was performed in the range of 150–2000 (m/z) at 70,000 resolution. Data were acquired with Xcalibur 2.0 software (Thermo Fisher Scientific K.K., Tokyo, Japan).

3. Results

3.1. Genome Analysis of Four Type Strains in the Genus Phytohabitans

Whole genomes of P. flavus NBRC 107702T, P. rumicis NBRC 108638T, P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T were sequenced by PacBio. Their genome sizes were 9.6 Mb, 10.7 Mb, 11.3 Mb and 10.2 Mb, respectively. The G+C contents ranged from 70.8 to 72.0%. Each genome encoded 10 to 18 PKS and NRPS gene clusters as summarized in Table 1. Type-II PKS gene clusters were not observed in the genomes.

Table 1.

Genomic features of strains used in this study.

Strains Genome Size (Mb) G+C Content Number of Gene Clusters
PKS NRPS Hybrid PKS/NRPS Total
I III I/III
P. flavus NBRC 107702T 9.61 70.8% 2 1 1 3 3 10
P. rumicis NBRC 108638T 10.71 71.1% 3 3 – 6 2 14
P. houttuyneae NBRC 108639T 11.34 71.6% 4 3 – 7 4 18
P. suffuscus NBRC 105367T 10.15 72.0% 2 2 – 5 5 14
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3.2. PKS and NRPS Gene Clusters Common between/among Species

Two type-I PKS (t1pks), two type-III PKS (t3pks), three NRPS (nrps) and one hybrid PKS/NRPS (pks/nrps) gene clusters were shared between/among multiple species (Table 2). T1pks-1, t3pks-1 and mrps-3 gene clusters were present in all the test strains. T1pks-1 gene cluster encoded only one PKS gene, whose domain organization is KS/AT/KR/DH. The unusual domain organization, such as not DH-KR but KR-DH and lack of ACP, is characteristic for the iterative PKS for enediyne synthesis [19]. The organization of adjacent genes is similar to those of maduropeptin, sporolide, calicheamicin and neocarzinostatin (Figure 1a). The phylogenetic analysis of the PKSs suggested those of t1pks-1 in P. flavus NBRC 107702T and P. rumicis NBRC 108638T is included in a clade of compounds with 9-membered enediyne moiety whereas those in P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T are closer to that of calicheamicin, which enediyne moiety is 10-membered (Figure 1b). Thus, the products of P. flavus NBRC 107702T and P. rumicis NBRC 108638T will be compounds similar to these 9-member enediyne compounds. In contrast, those of P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T would be different from them. T3pks-1 gene cluster encoded one type-III PKS, which is an ortholog of agqA for the synthesis of alkyl-O-dihydrogeranyl-methoxyhydroquinones. As this cluster also encoded orthologs of non-PKS/NRPS family genes, agqB to agqD [20] (Pfav_061719 to Pfav_06721, Prum_045400 to Prum_045380, Phou_043850 to Phou_045870, Psuf_029230 to Psuf_029250), the product was deduced to be alkyl-O-dihydrogeranyl-methoxyhydroquinones. Nrps-3 gene cluster resembled BGCs for siderophores, such as scabichelin and albachelin [21,22]. This cluster was predicted to synthesize a siderophore, composed of four to five amino-acid residues such as methyl-acetyl-hydroxy-ornithine (mHaOrn), methyl-ornithine (mOrn) and acetyl-hydroxy-ornithine (HaOrn) by antiSMASH analysis, although some monomers cannot be predicted. The selectivity-conferring codes [23] of A domains in the fifth modules was DAWEGGLVDK or DAWEVGLVDK, which is identical or quite similar to that of scabichelin-BGC (DAWEGGLVDK) loading hydroxy-ornithine (hOrn) [21]. Nrps-3 gene clusters of P. flavus NBRC 107702T, P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T likely share similar domain organizations (Ahaorn/MT/T–C/A/T–C/Aorn/MT/T–C/Ahaorn/T–C/A/T/E), whereas that of P. rumicis NBRC 108638T lacked C/A/T of the last module. Therefore, the products will be different between the three strains and P. rumicis NBRC 108638T, which are predicted as mHaOrn-x-mOrn-HaOrn-hOrn and mHaOrn-x-mOrn-HaOrn, respectively. Pks/nrps-3 gene cluster was present in three strains except for P. rumicis. This cluster harbors ten KR domains and eleven DH-KR domain pairs, catalyzing hydroxy groups and C=C double bond formations [7], respectively, were present as optional domains. Therefore, the product will be a large polyene compound, although it is unpredictable how the A domain in the last ORF is involved in the synthesis. It may suggest a novel function of A domain. T1pks-4 and nrps-4, t3pks-4 and nrps-11, and nrps-2 gene clusters were distributed between P. rumicis and P. houttuyneae, between P. houttuyneae and P. suffuscus, and between P. flavus and P. rumicis, respectively. T1pks-4 gene cluster encoded one PKS with single module, whose polyketide backbones were not predicted by their domain organization. Nrps-4 genes did not show high sequence similarities to published genes whose products are identified. However, based on the module numbers, the products were deduced to be a small molecule. T3pks-4 gene cluster encoded a type-III PKSs and combined with a terpenoid gene cluster. The hybrid cluster resembled diazepinomicin BGC, which suggests being responsible for the synthesis of the compound. Nrps-11 gene cluster did not show high sequence similarities to published genes whose products are identified. However, based on the domain organization, the product was deduced to be a nonapeptide, in which some amino acid residues may be modified by multiple C domains that were predicted to be involved in modification of the incorporated amino acid residues (CM). Nrps-2 gene cluster encoded seven NRPSs. According to the domain organization, which assembly line is T–C/A/T–C/Aasn/T–C/Aser/T–C/T–C/Aasn/T–C/Agly/T, the product is predicted to be a heptapeptide including two Asn, one Ser and one Gly residues. Nonribosomal peptides similar to those of nrps-2, -4 and -11 were not found in our database search using Norine.

Table 2.

Orthologous PKS and NRPS gene clusters between/among Phytohabitans species.

Gene Cluster ORF (Locus Tag) Domain Organization * Predicted Product
Pflav_ Prum_ Phou_ Psuf_
t1pks-1 005000 101970 010500 058040 KS/ATm/KR/DH enediyne-compounds
t1pks-4 n/a 07110 055560 n/a KS/ATp/DH/ER/KR/ACP unknown
t3pks-1 067180 045410 043880 029220 KS (type-III PKS) alkyl-O-dihydrogeranyl-methoxyhydroquinones
t3pks-4 n/a n/a 005750 091470 KS (type-III PKS) diazepinomicin
nrps-2 032950 078990 n/a n/a T s-x-Asn-Ser-x-Asn-Gly
032940 079000 LCL
032910 079030 A/T–LCL
032880 079150 Aasn/T
032770 079170 LCL/Aser/T–CM/A
032760 079180 T–CM/Aasn/T/–CM
032750 079190 Agly/T
nrps-3 036450 084390 072920 088300 Ahaorn/MT/T–DCL/A/T– siderophores such as mHaOrn-x-mOrn-HaOrn(-hOrn)
to to to CD/Aorn/MT/T–LCL/Ahaorn
036480 084420 088260 /T–DCL/A/T/E **
nrps-4 n/a 080570 069630 n/a FkbH/T s-y-Asx
080550 069620 LCL or LCL/T
080540 069610 T or LCL
080520 069600 LCL/Aasp/T–TE or Aasn/T
–TE
nrps-11 n/a n/a 067470 092920 T s-x-x-Thr-x-x-Orn-x-Ala-Asn
067480 092910 LCL
067520 092870 A/T–LCL/A/T
–092860
067530 092850 LCL/Athr/T–CM/A/T–CM/A
/T–CM/Aorn/T–CM
067540 092840 T–CM/Aala/T–CM/Aasn/T
–092820
pks/nrps-3 57090 n/a 95390 16680 KS/ATm/DH/KR/ACP Large polyene
to to to –KS/ATm/KR/ACP
57060 95400 16670 –KS ATp/KR/ACP
–KS ATm/KR/ACP
–KS/ATm/KR/ACP
–KS/ATm/KR/ACP
57050 95410 16660 KS/ATm/DH/ER/KR/ACP
to to to –KS/ATm/KR/ACP
57020 95440 16600 –KS/ATm/DH/KR/ACP
–KS/ATm/DH/KR/ACP
57010 95450 16590 KS/ATm/DH/ER/KR/ACP
–57000 –16580
56970 95480 16550 A
56960 95490 16540 AT
56950 95500 16530 ER
56890 95550 16480 ACP
to to to –KS/ATm/DH/KR/ACP
56870 95570 16470 –KS/ATm/DH/ER/KR/ACP
56860 95580 16460 KS/ATm/DH/ER/KR/ACP
–56840 –95600 –16450 –KS/ATm/DH/KR/ACP
56830 95610 16430 KS/ATm/KR/ACP
to to to –KS/ATm/KR/ACP
56820 95640 16420 –KS/AT/KR/ACP
–KS/ATp/KR/ACP
56810 95650 16410 KS/ATm/DH/KR/ACP
to to –KS/ATm/DH/KR/ACP
56790 16390 –KS/ATm/DH/KR/ACP
–KS/ATm/DH/KR/ACP
–KS/ATm/DH/KR/ACP
56780 95660 16380 KS/ATm/DH/KR/ACP
–16350
56630 95800 16270 ACP
56620 95810 16260 KS
56600 95830 16240 A–TE
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* Typical domain organizations are shown as slight differences were observed between/among strains. ** Domain organization of nrps-3 gene cluster in P. rumicis NBRC 108638T was A/MT/T–CM/A/T–CM/A/MT/T–CL/A/T/E. Slash is inserted between domains, whereas hyphen is between modules. Amino acid residues in italics were predicted only by antiSMASH. Abbreviations: A, adenylation; Aad, 2-aminoadipic acid; ACP, acyl carrier protein: AHBA, aminohydroxybenzoate; Asx, Asp or Asn; AT, acyltransferase; ATe, AT for ethylmalonyl-CoA; ATm, AT for malonyl-CoA; ATp, AT for methylmalonyl-CoA; C, condensation; CCy, heterocyclization (Cyc) domain that catalyze both peptide bond formation and subsequent cyclization of cysteine, serine or threonine residues.; DCL, C domain that link an L-amino acid to a growing peptide ending with a D-amino acid; CDu, dual E/C domain that catalyze both epimerization and condensation; LCL, C domain that catalyze a peptide bond between two L-amino acids; CM, C domain that appears to be involved in the modification of the incorporated amino acid, for example the dehydration of serine to dehydroalanine; CS, starter C domain (first dominated and classified as a separate subtype here) which acylates the first amino acid with a β-hydroxy-carboxylic acid (typically a β-hydroxyl fatty acid); CoL, CoA-ligase; DH, dehydratase; Dha, dehydroalanine; DHB, hydroxybenzoate; dVal, D-Val; dx, D-amino acid; E, epimerase; ER, enoylreductase; HaOrn, acetyl-hydroxy-Orn; hOrn, hydroxy-Orn; KS, ketosynthase; KS1, KS domain present in the first module of assembly lines; KR, ketoreductase; mHaOrn, methyl-HaOrn; mOrn, methyl-Orn; MT, methyltransferase; mx, methyl-amino acid; n/a, not present; Orn, ornithine; pk, polyketide moiety; s, starter molecule; T, thiolation (peptidyl carrier protein); TE, thioesterase; TD, termination domain; x, unidentified amino acid residue; y, unknown residue due to the lack of A domain. Inferior 3-letter-abbriviated amino acids just after A domains are substrates of the A domain.

Figure 1.

Figure 1

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Comparison between t1pks-1 gene clusters and reported enediyne type-I PKS gene clusters. (a) Gene organization. pink, DUF1702 family protein/enediyne biosynthesis protein; black, type-I PKS; red, thioesterase; light blue, flavin reductase, oxidoreductase or FAD-dependent monooxygenase; yellow, cytochrome P450; green, transcriptional regulator; white and grays, others. Homologous hypothetical genes are colored in dark gray or light gray, respectively. (b) Phylogenetic analysis of type-I PKSs. The phylogenetic tree was reconstructed by the neighbor-joining method using ClustalX 2.1. Numbers on the branches represent the confidence limits estimated by bootstrap analysis with 1000 replicates; values above 50% are at branching points. Accession numbers of used sequences are as follows: MdpE, AAQ17110; Strop_2697, ABP5514; SgcE, AAL06699; NcsE, AAM78012; CalE8, AAM94794; AcmE, ATV95639; KedE, AFV52145; UcmE, AMK92560; DynE, AAN79725. Kedarcidin also includes 9-membered enediyne moiety whereas the enediyne moieties of calicheamicin, uncialamycin and dynemicin are 10-membered.

3.3. PKS and NRPS Gene Clusters Specific to Each Strain

3.3.1. P. flavus NBRC 107702T

Five gene clusters were specific to P. flavus NBRC 107702T (Table 3). T1pks-2 gene cluster encoded AT-less PKSs. The domain organization of Pfav_13200 to Pfav_13340 was similar to that of PKS for anthracimycin synthesis [23]. However, this cluster encodes additional PKSs (Pfav_012890 to Pfav_012980), which are not present in the anthracimycin biosynthetic gene cluster (BGC). Thus, the product was predicted to be a larger polyketide than anthracimycin, which includes an anthracimycin-like moiety as a part. T1pks/t3pks was a hybrid gene cluster encoding 21 type-I PKSs and one type-III PKS. The type-I PKS harbors five KR domains and nine DH-KR domains. Hence, the product will be a large polyene compound whose starter unit is a chalcone-like moiety derived from type-III PKS. Nrps-1 gene cluster harbored less than two modules. Hence, the product would be simple. Pks/nrps-1 gene cluster encoded two hybrid PKS/NRPS proteins. They are predicted to form only two modules, which load AHBA and methylmalonyl-CoA, respectively. The molecule synthesized by this cluster would be small and simple. Pks/nrps-2 gene cluster encoded six NRPSs and one PKS. They included one loading module, one PKS module and five NRPS modules and it is deduced to synthesize a peptide containing one Asp and two Ser molecules and a polyketide unit. Hybrid polyketide/nonribosomal peptide compounds resembling that of pks/nrps-2 were not found in our database search.

Table 3.

PKS and NRPS gene clusters specific to P. flavus NBRC 107702T.

Gene Cluster ORF (Pflav_) Size (aa) Domain Organization Deduced Product
t1pks-2 012890 2993 KS/DH/KR/ACP–KS/KR/ACP–KS large polyketide with anthracimycin-like moiety
012900 3001 DH/ACP–KS/DH
012920 2707 KR/ACP–KS/ACP–KS/DH/KR/ACP–KS
012930 832 ACP–KS
012940 820 KR/ACP
012950 1099 KS/DH/KR
012960 1301 MT/ACP–KS/DH/ACP
012970 535 KS
012980 117 ACP
013200 893 ATm/ATm
013220 3254 KS/KR/ACP–KS/DH/KR/ACP–KS
013230 1768 DH/KR/MT/ACP
013240 985 ER–KS/DH
013260 1140 ACP–KS/DH
013270 1303 KR/ACP–KS/ACP
013280 892 KS/DH
013290 909 KR/MT
013300 320 KS
013310 1302 DH/KR/ACP
013320 833 KS/ACP
013220 554 KS
013340 756 ACP/TE–MT
t1pks/t3pks 008030 * 369 KS (type-III PKS) large polyene with a starter derived from type-III PKS
008050 2178 CoL/KR/ACP–KS/ATp/DH
008060 3857 KR/ACP–KS/ATp/DH/KR/ACP
–KS/ATm/KR/ACP
008070 3045 KS/ATp/DH/ER/KR/ACP–KS/ATm
008080 4076 KR/ACP–KS/ATm/DH/KR/ACP
–KS/ATm/DH/KR/ACP
008090 5897 KS/ATp/DH/KR/ACP–KS/ATm/KR/ACP
–KS/ATp/DH/KR/ACP–KS/ATm/ACP
008100 377 KS
008110 1236 ATp/DH/KR/ACP
008130 250 KS
008140 865 ATm/DH
008150 419 ACP–KS
008190 3436 KR/ACP–KS/ATm/DH/KR/ACP
–KS/ATm/DH
008200 1003 ER/KR/ACP
008210 425 KS
008220 490 ATp
008240 1407 DH/KR/ACP–KS
008250 2346 ATm/KR/ACP–KS/ATm/KR/ACP
008260 319 KS
008270 2499 ATm/DH/KR/ACP–KS/ATm/DH
008280 1703 ER/KR/ACP–KS/ATm
008290 976 ER/KR
008300 356 ACP/TE
nrps-1 004670 * 93 T s-x
004680 1055 CL/A/T
004700 452 CL
pks/nrps-1 010020 1437 CoLAHBA/ACP–KS/ATp AHBA-pk
010030 551 ACP–LCL
pks/nrps-2 015420 1122 T–LCL/A/T s-x-pk-Asp-y-Dha-Dha
015410 1831 KS/ATm/KR/DH/ACP
015390 284 LCL
015380 1445 Aasp/T–LCL
015370 725 T–CM
015360 780 Aser/T
015350 1329 CM/Aser/T–TE
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* Encoded in the complementary strand. Abbreviations are the same as those of Table 2.

3.3.2. P. rumicis NBRC 108638T

One t1pks, two t3pks, three nrps and two pks/nrps gene clusters were specific to P. rumicis NBRC 108638T (Table 4). T1pks-3 gene cluster resembled pyrrolomycin BGC and their domain organizations were the same. Therefore, it will be responsible for the synthesis of pyrrolomycin. The products of t3pks-2 and -3 gene clusters were not able to be predicted by this bioinformatic analysis. However, as t3pks-2 gene cluster also encoded terpenoid-biosynthetic genes, we predicted the product to be a terpenoid with a polyketide moiety derived from type-III PKS. The products of nrps-5, -6 and -7 gene clusters were predicted to be tetrapeptides as shown in Table 4. Similarly, the products of pks/nrps-4 and -5 were deduced to be tetra- and penta-peptides, respectively, with a polyketide moiety. Nonribosomal compounds like those of nrps-5, nrps-6, nrps-7, pks/nrps-4 and pks/nrps-5 were not found in our database search.

Table 4.

PKS and NRPS gene clusters specific in P. rumicis NBRC 108638T.

Gene Cluster ORF (Prum_) Size (aa) Domain Organization Deduced Product
t1pks-3 052570 376 KS pyrrolomycin
052590 423 KS
052640 1481 ATm/ACP–KS/ACP
052650 2081 KS/ATm/DH/KR/ACP–TD
t3pks-2 009490 356 KS (type-III PKS) terpenoid with pk moiety
t3pks-3 005640 359 KS (type-III PKS) unknown
nrps-5 073950 * 497 A x-y-Cys-x
074040 * 89 T
074060 556 LCL/T
074070 563 LCL
074090 1538 T–CM/A/T–TE
074100 544 Acys
nrps-6 073810 * 2114 LCL/Aphe/T–LCL/A/T Phe-x-Ser-x
073870 2381 LCL/Aser/T–CM/A/T–TE
nrps-7 005920 514 A x-Gly-Gly-x
006040 * 865 T–TE
006050 * 971 LCL/A
006060 * 1054 LCL/Agly/T
006070 * 450 LCL
006090 541 LCL
006100 464 Agly/T
006110 85 T
pks/nrps-4 021280 1995 CS/A/T–LCL/Aphe x-Phe-x-Phe-pk
021270 2780 T–LCL/A/T/E–DCL/Aphe/T
021190 1102 KS/AT
021180 410 KR/ACP
021250 443 ER
pks/nrps-5 011340 1837 KS/ATm/KR/DH/ACP pk-Ser-x-Ser-Gly-x
011290 * 2046 Agly/T–LCL/A
011280 887 LCL/Aser
011270 317 T–LCL
011260 831 A/T
011250 1718 LCL/Aser/T–CM
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* Encoded in the complementary strand. Abbreviations are the same as those of Table 2.

3.3.3. P. houttuyneae NBRC 108639T

Two t1pks, one t3pks, five nrps and three pks/nrps gene clusters were specific to P. houttuyneae NBRC 108639T (Table 5). T1pks-5 encoded one PKS with single module, whose polyketide backbones were not predicted by their domain organization. T1pks-6 gene cluster showed similarity to deschlorothricin-BGC. However, as their domain organizations were different each other, the product of t1pks-6 will not be deschlorothricin but a deschlorothricin-like compound. Since t3pks-4 gene cluster did not show high amino acid sequence similarities to product-identified gene clusters, its product was not able to be speculated. Nrps-8, -9, -10 and -12 gene clusters also did not show high similarities to gene clusters whose products are identified. However, according to the domain organizations and/or substrates of A domains, their products were deduced to be di-, nona-, penta-, and penta-peptides, respectively, as shown in Table 5. Pks/nrps-7 gene cluster encoded ten NRPSs harboring multiple domains, forming 24 NRPS modules, and one type-III PKS. Hence, it will synthesize a large peptide composed of 24 amino-acid residues with a polyketide moiety derived from type-III PKS. In contrast, pks/nrps-6 and -8 gene clusters encoded less NRPSs and their products were predicted to be tri-, and tetra-peptides with a moiety derived from each small PKS, respectively. Nonribosomal peptide- and/or hybrid polyketide/nonribosomal peptide-compounds shown as deduced product in Table 5 were not found in our database search.

Table 5.

PKS and NRPS gene clusters specific to P. houttuyneae NBRC 108639T.

Gene Cluster ORF (Phou_) Size (aa) Domain Organization Deduced Product
t1pks-5 056050 2029 KS/ATm/DH/ER/KR/ACP unknown
t1pks-6 049460 * 1704 KS1/AT/DH/KR/ACP deschlorothricin-like polyketide
049580 3493 KS/ATm/ACP
–KS/ATm/DH/KR/ACP
–KS/ATe
049590 1347 DH/ER/KR/ACP
049600 3825 KS/ATp/DH/KR/ACP
–KS/ATm/DH/ER/KR/ACP
049630 3144 DH/KR/ACP
–KS/ATp/DH/ER/KR/ACP
049640 1512 KS/ATp/KR/ACP
049700 * 1537 KS/ATm/ACP
049740 * 820 DH/KR
049750 * 841 KS/ATm
049760 * 2148 KS/ATp/DH/ER/KR/ACP
049770 * 2263 KR/ACP–KS/ATp/KR/ACP
049780* 2211 KS/ATm/KR/ACP–KS
t3pks-4 014220 245 KS (type-III PKS) unknown
nrps-8 083430 1179 CS/A/T x-x
083460 528 A
nrps-9 077860 1332 A/T–LCL/A x-x-dVal-dVal-x-dx-Thr-Val-x
077870 4920 T/E–DCL/Aval/T/E–DCL/Aval/T/E–DCL/A/T
077880 2628 LCL/A/T/E–DCL/Athr/T–LCL
077890 3704 A/T/E–DCL/Aval/T–LCL/A/T/E
nrps-10 004780 1019 LCL/Agly/T pentapeptide containing Gly and Cys
004790 569 A/T
004800 167 T
004810* 2225 Acys/T–TE–LCL/A/T
004820* 628 LCL
004830* 463 LCL
004840 413 A
nrps-12 052350 * 590 Aval/T Val-x-y-x-x
052430 606 A/T
052440 1105 LCL/T–LCL
052470 611 A/T
052540 477 LCL
052560 682 A/T–TE
pks/nrps-6 078860 * 184 ER Ala-Leu-x-pk
078970 407 Aala
078980 1282 T–LCL/Aleu/T
078990 1277 LCL/A
079000 236 T
079010 759 KS/ATm
079030 94 ACP
079050 359 FkbH
079160 284 KR
pks/nrps-7 020430 3673 LCL/A/T–LCL/Aasp/T–LCL/A/T–LCL x-Phe-Asp-Asp-x-Asp-x-Gly-Leu-Tyr-Thr-x-Asp-Gly-Asp-x-x-x-x-Thr-Tyr-Asp-Tyr-Asp with pk
020420 1353 Agly/T–LCL/Aleu
020410 3833 T–LCL/Atyr/T–LCL/Athr/T–CDu/A/T–LCL
020400 2741 Aasp/T–LCL/Agly/T–LCL/Aasp/T
020370 4620 CDu/A/T–LCL/A/T–CDu/A/T–LCL
020360 1578 Athr/T–LCL/Atyr
020350 459 T–LCL
020340 3163 Aasp/T–LCL/Atyr/T–LCL/Aasp/T–TE
020260 2056 CS/Aphe/T–LCL/Aasp/T
020250 1041 LCL/Aasp/T
020190 375 KS (type-III PKS)
020170* 492 A
020130* 106 T
020120 104 T
pks/nrps-8 022380 471 LCL x-Gly-pk-Gly-x
022350 1042 LCL/Agly/T
022330 661 LCL
022320 398 T
022310 872 T–KS/ATm
022300 1041 DH/KR/ACP
022280 * 1004 LCL/Agly/T
022270 87 T
022260 * 506 A
022210 296 A
022190 507 T–LCL
022170 * 352 T–TE
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* Encoded in the complementary strand. Abbreviations are the same as those of Table 2.

3.3.4. P. suffuscus NBRC 105367T

One t1pks, four nrps and four pks/nrps gene clusters were specific to P. suffuscus NBRC 105367T (Table 6). T1pks-7 gene cluster encoded 16 PKS proteins, whose modules were twelve. Since there are six DH-KR pairs, yielding C=C double bonds, this product will be a polyene polyketide. Nrps-14 was assigned to be a BGC for pentapeptides as shown in Table 6. As nrps-14 gene cluster was similar to BGC for cephamycin, we considered it to be a cephamycin BGC. Nrps-15 gene cluster encoded four NRPSs, two of which included a terminal TE domain, respectively. Although it is unclear which TE of the two is functional, we predicted the product to be DHB-Ser based on ORFs of Psuf_002170, Psuf_002160 and Psuf_002150. Such a part is often observed in siderophores. By catalyzing iteratively, this cluster may synthesize a siderophore like enterobactin, which is composed of three pairs of DHB-Ser. Pks/nrps-9 gene cluster encoded one iterative PKS for enediyne and one type-III PKS in addition to 13 NRPSs for a total number of module of six. The product would be a hexapeptide including Ser, Cys, Pro as the amino-acid residues, a polyketide component derived from type-III PKS, and an enediyne moiety. Although the product of pks/nrps-10 gene cluster was unclear, it will be a polyketide with a thiazoline residue formed by cyclization of Cys. Pks/nrps-11 gene cluster was considered to be a chlorizidine BGC according to the similarity between their gene organizations. Pks/nrps-12 gene cluster encoded 22 proteins, whose PKS modules were 13, and one NRPS. In the PKS domain organization, four KR domains and four DH-KR domain pairs were present, suggesting the product to be a polyene compound with a moiety derived from Leu. Deduced products of nrps-13, pks/nrps-9, pks/nrps-10 and pks/nrps-12 were not reported in our database search.

Table 6.

PKS and NRPS gene clusters specific in P. suffuscus NBRC 105367T.

Gene Cluster ORF (Psuf_) Size (aa) Domain Organization Deduced Product
t1pks-7 066740 406 KS1 polyene derived from C24 polyketide chain
066760 1871 ATm/ACP–KS/ATp/DH/KR
066770 2858 ACP–KS/ATp/DH/KR/ACP–KS/ATm/KR
066780 1414 ACP–KS/ATp/DH
066790 380 KR/ACP
066800 2229 KS/ATp/DH/KR/ACP–KS
066810 1470 ATp/DH/ER/KR/ACP
066820 235 KS
066830 433 ATm
066840 986 DH/KR/ACP
066850 1844 KS/ATp/DH/KR/ACP
066860 764 KS/ATp
066870 230 KR
066880 282 ACP
066890 702 KS
066900 655 KR
066910 2409 ACP–KS/ATe/DH/ER/KR/ACP–TE
nrps-13 065520 * 922 LCL/A s-x-Leu-x-y-Ser
065480 * 675 Aleu/T
065440 1103 T–LCL/T
065390 * 466 A/T
065370 753 DCL/Aser
065360 291 T
065270 792 Aleu/T
065190 2256 CoL/T–LCL/A/T–LCL
nrps-14 059700 3735 Aaad/T–DCL/Acys/T–LCL/Aval/T/E–TE cephamycin
nrps-15 0021240 * 852 A/T–TE DHB-Ser
0021170 556 Adhb
0021160 299 T
0021150 1293 CS/Aser/T–TE
pks/nrps-9 070000 1920 KS/ATm/KR/DH hexapeptide including Ser, Cys, Pro, pk and enediyne-moiety
070250 * 382 KS (type-III PKS)
070260 * 463 LCL
070270 * 588 A/T
070280 533 T–LCL
070350 1174 Aser/T–LCL
070360 361 A/T
070410 872 Acys/T
070420 534 T–LCL
070430 439 LCL
070440 97 T
070450 527 A
070460 451 LCL
070490 532 Apro
070520 89 T
pks/nrps-10 018900 * 747 ER/KR/ACP polyketide including a thiazoline residue
018190 * 1328 KS/ATp/DH
018880 * 1251 ATp/KR/ACP
018870 * 1643 KS/AT/ACP–KS
018860 1779 KS/ACP–CCy/Acys/T
018830 384 ATm
018820 606 ACP–KS
018810 1588 ATp/DH/ER/KR
018800 353 KS
018790 791 ATp
018780 362 KR/ACP
018750 * 87 ACP
018720 492 A
pks/nrps-11 004960 150 ATm chlorizidine
005010 * 501 A
005100 1489 KS/AT/ACP–KS
005110 1223 AT/DH/KR
005120 123 ACP
005130 294 KS
005140 380 KS
005150 795 ATp/ACP–TD
005190 85 ACP
005210 333 KS
005190 1358 Agln/T
pks/nrps-12 000760 602 Aleu/T likely polyene with Leu
000690 1757 KS/AT/DH/KR/ACP
000570 399 KS
000560 1292 ATp/DH/KR/ACP
000540 335 ATp
000530 967 DH/ER/KR
000520 206 ACP
000510 1267 KS/ATp
000500 237 ACP
000460 * 90 ACP
000400 * 911 KS/ACP
000370 * 1379 ATp/DH/KR/ACP
000360 * 409 KS
000350 * 2152 KS/ATp/DH/ER/KR/ACP
000330 * 2862 KS/ATm/KR–KS/ATm/KR/ACP
000320 * 1727 KS/ATm/KR/ACP
000250 2982 KS1/AT/ACP–KS/ATp/KR/ACP–KS
000240 617 ATp/DH
000230 553 KR
000220 2051 KS/ATm/DH/ER/KR/ACP
000180 * 448 ER
000160 * 89 ACP
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* Encoded in the complementary strand. Abbreviations are the same as those of Table 2.

3.4. Genomic Positions of the Gene Clusters

Genomic positions of the PKS and NRPS gene clusters were diagrammatically shown in Figure 2. Orthologous clusters present between/among the strains are connected by line in the figure. All the strains harbored t1pks-1, t3pks-1 and nrps-3 gene clusters. Pks/nrps-3 were present in three strains except for P. rumicis NBRC 108638T. Nrps-4 and t1pks-3 were distributed between P. rumicis NBRC 108638T and P. houttuyneae NBRC 108639T, whereas t3pks-4 and nrps-11 were between P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T. The remaining 31 gene clusters were not shared between different species: five, eight, ten and eight were specific to P. flavus NBRC 107702T, P. rumicis NBRC 108638T, P. houttuyneae NBRC 108639T and P. suffuscus NBRC 105367T, respectively, as shown by closed circles in the figure.

Figure 2.

Figure 2

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Positions of PKS and NRPS gene clusters in chromosomes of (F) P. flavus NBRC 107702T, (R) P. rumicis NBRC 108638T, (H) P. houttuyneae NBRC 108639T and (S) P. suffuscus NBRC 105367T. Chromosome or scaffold sequences are indicated by black and bold horizontal lines. Red, PKS gene cluster; blue, NRPS gene cluster; green, hybrid PKS/NRPS gene cluster. The cluster numbers are the same as those in Table 2, Table 3, Table 4, Table 5 and Table 6. Gene clusters specific to each strain are shown by filled circles. Orthologous gene clusters are shown by open circles and connected between strains by lines. Alignments and direction of scaffold sequences in R and H are putative because their whole genome sequences are not complete.

3.5. Production of Unknown Compounds

The four strains were cultured on two kinds of agar medium. The growths of P. flavus NBRC 107702T and P. rumicis NBRC 108638T were poor compared with the other two strains. The culture extracts were analyzed by LC-MS. Ion peaks corresponding to [M+H]+ of known compounds, such as alkyl-O-dihydrogeranyl-methoxyhydroquinones (exact mass; 486.41, 500.42, 556.49, 570.50), diazepinomicin (462.25), pyrrolomycins (353.91, 322.91, 305.94 etc.), cephamycins (579.15, 446.11, 659.11), enterobactin (669.14) and chlorizidines (441.94, 415.97), were not observed. In contrast, the other ion peaks were observed, among which we here picked up ones listed in Table 7. Ion peaks of m/z 656.31 eluted at 2.8 min (3) were observed in the culture extracts of the three strains except for P. rumicis NBRC 108638T whereas ion peaks of 1 and 2 were observed specifically in that of P. rumicis NBRC 108638T. Ion peaks (4) and (5) were specific for P. suffuscus NBRC 105367T and P. houttuyneae NBRC 108639T, respectively. We searched reported compounds with these accurate mass values in the database of Dictionary of Natural Products and consequently there are not significant hits, suggesting that these compounds are likely novel.

Table 7.

Representative ion peaks in the LC-MS analysis.

Retention Time Observed Ion Peak (m/z)
P. flavus NBRC 107702T P. rumicis NBRC 108638T P. houttuyneae NBRC 108639T P. suffuscus NBRC 105367T
2.2 min (1) – 597.29 t – –
2.5 min (2) – 554.28 t – –
2.8 min (3) 656.31 t – 656.31 t 656.31 t
6.3 min (4) – – – 505.40 t, i
7.2 min (5) – – 812.44 t, i –
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–, not observed; t and i, observed when cultured on double diluted TSA and double diluted ISP-2 agar, respectively.

4. Discussion

In conventional screenings for novel secondary metabolites, re-isolation of known compounds has been problematic. This caused a change in the strategies used for natural product discovery by shifting to new sources as producing microorganisms. Prediction of products based on smBGCs, such as PKS and NRPS gene clusters, is a powerful approach to reduce the frequency to isolate known compound although further investigations need to be carried out.

Here, we sequenced whole genomes in four type strains of the genus Phytohabitans, which have not been studied by genome sequence-based strategies, by PacBio, analyzed their PKS and NRPS gene clusters and bioinformatically predicted the chemical structures of the products derived from these gene clusters. Fifty-six gene clusters were identified from the four strains, which are involved in the biosynthesis of 40 different types of polyketide and/or nonribosomal peptide compounds. Although analysis focusing on the domain organizations and bioinformatical substrate prediction is not sufficient to conclude the products are the same because of possible variants derived from low substrate selectivity of A and AT domains, few gene clusters were shared between/among different species. Each strain harbored five to eleven specific gene clusters. Most of the gene clusters are not for known compounds and their predicted chemical structures are novel. Among the 40 biosynthetic gene clusters, only six were identified to produce known products. These known compounds were not produced in our culture conditions. These BGCs may be cryptic in the condition and/or their productivity may too low to detect them in samples derived from small scale cultures. To express these BGGs and/or produce more, further investigations are necessary. The duplication of the putative metabolites within the genus were only nine as shown in Table 2, suggesting many are specific in each species. Therefore, members of the genus Phytohabitans are considered as an attractive source for novel and diverse secondary metabolites. To confirm it, we analyzed the culture extracts by LC-MS as a preliminary study. As expected, ion peaks corresponding to some putative novel compounds were observed. We are guessing that the products of ion peaks 1 to 3 are siderophores derived from nrps3. Nrps-3 gene cluster is distributed to the four strains but that in P. rumicis NBRC 108638T lacks the fifth module and its product will be smaller than the others. Nrps-3 resembles that of scabichelin, whose exact mass is 647.36. Although the second amino acid residue of the product by nrps-3 was unpredictable in this study, the exact mass will be close to that of scabichelin because they are similar siderophores. Thus, the compound of m/z 656.31 is plausible as the product. Furthermore, P. rumicis NBRC 108638T, whose nrps-3 lacks the fifth module, did not produce the product of m/z 656.31, but produced smaller ones, which can be account for by the absence of the fifth module. Unfortunately, it is not possible to determine chemical structures of final products because PKS and NRPS assembly lines determine chemical structures of the backbones [7], but do not those of final products since the backbones are usually modified by other enzymes to yield the final products. It is unclear at present which gene clusters in P. suffuscus NBRC 105367T and P. houttuyneae NBRC 108639T synthesize the two putative novel compounds (4, 5). Except for siderophores, remarkable ion peaks with high intensities were not observed from P. flavus NBRC 107702T and P. rumicis NBRC 108638T. This may be due to their poor growth in our culture conditions.

Compared with general type-I PKSs and NRPSs, some of those in the genus Phytohabitans were observed to split on many proteins. It is still unclear if it is artifact from sequencing and/or assembly technologies. However, obvious ORFs that are likely involved in biosynthetic pathway, such as accessory enzymes, were not observed between such the split PKS and NRPS genes. To confirm whether modular enzyme genes are often split in the genus Phytohabitans or whether it is due to technological artifact(s), more reliable method(s) should be employed.

During this study, a novel species Phytohabitans kaempferiae was reported, which is an endophytic actinomycete isolated from the leaf of Kaempferia larsenii [24]. Although the whole genome has yet to be sequenced, the analysis will also reveal further potential of the genus because different species, in general, harbor specific PKS and NRPS pathways, as shown in this and our previous studies on actinomycetes [15,16,17].

Acknowledgments

We thank Aya Uohara for registering the genome sequences in the DDBJ.

Author Contributions

Conceptualization, H.K. and T.T.; methodology, H.K. and T.T.; formal analysis, H.K.; investigation, H.K.; resources, T.T.; data curation, H.K.; writing—original draft preparation, H.K.; writing—review and editing, T.T.; funding acquisition, T.T. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported in part by the commissioned project from the Japan Patent Office.

Conflicts of Interest

The authors declare no conflict of interest.

Footnotes

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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