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. 2017 Aug 10;7:7851. doi: 10.1038/s41598-017-08463-3

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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(A) Log transformation of the fold change in transcript abundances obtained through microarray and qRT-PCR indicates consistency in the results obtained through both techniques (B) Heat map displaying normalized changes in transcript abundances for a subset of genes implicated in nitrogen metabolism. Highest obtained values under non-limiting nitrogen conditions corresponded to genes related to ammonium transport (amtB, ammonium transporter gene; PRU_1977, hypothetical transporter), ammonium assimilation and its regulation (PRU_2048, NAD-dependent glutamate dehydrogenase; PRU_2071, gdhA, NADP-dependent glutamate dehydrogenase; glnA, glutamine synthetase type I; glnN-1 glutamate synthetase type III-1; glnN-2 glutamate synthetase type III-2; gltB, glutamate synthase, large subunit; gltD, glutamate synthase, small subunit; glnK, nitrogen regulatory protein P_II), amino acid and protein biosynthesis (dapF, diaminopimelate epimerase; asnB, asparagine synthase; PRU_1974, aminotransferase, homolog; PRU_1973, glutamine amidotransferase). Highest values under growth on peptides corresponded to genes involved in protein biosynthesis (PRU_2971, O-acetylhomoserine aminocarboxypropyltransferase; cysK, cysteine synthase; PRU_2042, diaminopimelate dehydrogenase), or had unclear roles in nitrogen metabolism (PRU_2827, outer membrane receptor RagA) (H, growth on excess ammonium; L, growth on limiting ammonium concentrations; A, growth on ammonium; P, growth on peptides). (C) Comparison of log transformed fold changes in transcript abundances obtained by qRT-PCR in the assayed growth conditions (AP, Ammonium vs Peptides, HL, excess (H) vs growth-limiting (L) ammonium concentrations). Gene symbols and observed trends as in (B). (D) Principal component analysis integrating fold change in transcript abundances obtained through microarray and qRT-PCR on P. ruminicola 23 grown in different nitrogen sources (ammonium or peptides) or ammonium concentrations (excess [high] or growth-limiting [low]). Arrows point in the direction of the maximum correlation. Gene symbols as in (B) and (D).