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. 2025 Sep 26;16:8527. doi: 10.1038/s41467-025-64086-7

Table 1.

Selected RNA-dependent candidates based on RAPDOR analysis and manual filtering

Protein ANO JSD Shift Rank SVM Comments and annotation
Sll1967 1 0.85 − 4 2 282 RNA methyltransferase RlmD, Co-enriched with the RNase P-interacting protein YlrR/Ssr123838
*Slr1531 1 0.74 + 12 6 19 Signal recognition particle protein Ffh
Slr0355 1 0.71 + 6 8 n/a (S)-8-amino-7-oxononanoate synthase BioU
Sll1371 1 0.7 − 3.16 9 n/a SyCrp1 transcription factor
Ssl2245 1 0.34 − 3 23 n/a Putative antitoxin57
Slr0711 0.96 0.16 − 4.58 33 n/a 7-cyano-7-deazaguanine reductase QueF
Sll1315 0.93 0.63 − 12 35 n/a WD40 repeat protein
Sll7087 0.93 0.39 − 9.99 38 n/a CRISPR-Cas protein Cmr4
Slr0670 0.93 0.33 − 3.97 39 n/a Universal stress protein
*Ssr3189 0.89 0.39 − 9.26 44 n/a Homolog Asl3888 in Nostoc 7120 was validated as RBP in PNK assay46
Slr0147 0.85 0.37 − 3.94 53 n/a 4-vinyl reductase
Slr0782 0.85 0.28 − 3 55 n/a L-amino acid dehydrogenase
Sll0947 0.81 0.35 − 13 59 n/a Ribosome hibernation factor (Hpf/RaiA/LrtA)
Sll0517 0.78 0.26 − 5.3 67 16 Cold-induced RRM protein RbpA/Rbp149
Ssl3335 0.78 0.2 − 12.48 72 n/a preprotein translocase subunit SecE
Sll0726 0.78 0.16 − 3 73 n/a Phosphoglucomutase, Pgm
*Slr2130 0.74 0.3 − 3 76 n/a AroB, 3-dehydroquinate synthase
Sll1961 0.7 0.38 − 12 85 n/a GntR-type transcriptional regulator60
Slr1265 0.56 0.13 − 4.81 129 n/a RNAP subunit gamma RpoC1
Slr1030 0.44 0.28 − 13 174 228 Mg2+ chelatase subunit ChlI

After removing ribosomal proteins, 20 proteins with a promising rank in the RAPDOR analysis are given together with their SVM prediction of RNA binding (Supplementary Data 2). The gene name or locus tag is given, followed by the ANOSIM R value (ANO), the mean JSD, the relative shift in the number of fractions, the absolute rank assigned by RAPDOR and SVM, comments and annotation. n/a indicates an SVM score below the threshold.

Asterisks indicate that the homologs in Nostoc 7120 also showed RNA-dependent shifts46. See also Figs. 5 and 6 and Supplementary Data 2. Boldface letters indicate RBPs validated in PNK assays (Fig. 7).