Functional classification of genes regulated in an RpoH1-dependent manner The 101 genes that had distinct expression profiles in the rpoH1 mutant arrays in comparison to the wild type, ergo genes that presented an RpoH1-dependent
expression, were also grouped according to their COG classification. The COG classification distributes genes in orthologous groups on basis of functional predictions and patterns of sequence similarities . The RpoH1-dependent genes were assigned to 18 functional categories, indicating a global effect on gene expression dependent on RpoH1 upon pH shock. Among BMN 673 mw the known most representative classes were protein turnover and chaperones, followed by translation, transcription and by transport and
metabolism of carbohydrates, nucleotides and amino acids (Figure 7). There C646 purchase is indeed a dramatic increase in the expression of chaperone proteins and heat shock genes in response to pH shock. A total of 24 genes that presented an RpoH1-dependent upregulation following acid shift are involved in heat shock and stress response. Among the proteases, the genes coding for HtpX, a membrane-bound and stress-controlled protease well characterized in E. coli , as well as those coding for ClpB and ClpP2, responsible for disassembling protein aggregates that accumulate in the cytoplasm under stress conditions , were expressed in dependence of RpoH1. The operon formed by the genes hslUV, which codes for an intrinsic URMC-099 nmr ATP-dependent proteasome system for degradation of misfolded proteins in the cytoplasm, was Thymidine kinase also upregulated in an RpoH1-dependent fashion. Among the induced chaperones were also the gene Smc00699, coding for a heat shock DnaJ-like protein, as well as the
gene coding for GrpE, which is part of the cellular chaperone machinery capable of repairing heat-induced protein damage . Moreover, there was an RpoH1-dependent upregulation of the operon that codes for the only GroELS proteins specialized in stress response in S. meliloti, GroELS5 . The gene coding for the small heat shock protein IbpA  was also upregulated. Genes like groEL5 and clpB have already been described as genes whose transcription is RpoH1-dependent in S. meliloti [22, 25]. The group of proteins shown to be involved in the heat shock response under the transcriptional control of RpoH usually includes chaperones, proteases, and regulatory factors . The mutation in the rpoH1 gene in S. meliloti and its characterization under pH stress revealed indeed a lack of activation of all major types of regulatory chaperones and key heat shock proteins usually activated in stress conditions. In the present study, we have seen representatives of all of those groups to be involved in pH stress response. We hence attest to the role of rpoH1 in S. meliloti pH stress response as being evidenced by the activation of acid-induced heat shock proteins and chaperones in dependence of rpoH1 expression.