Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria

Abstract

In proteobacteria, genes whose expression is modulated in response to the external concentration of inorganic phosphate are often regulated by the PhoB protein which binds to a conserved motif (Pho box) within their promoter regions. Using a position weight matrix algorithm derived from known Pho box sequences, we identified 96 putative Pho regulon members whose promoter regions contained one or more Pho boxs in the Sinorhizobium meliloti genome. Expression of these genes was examined through assays of reporter gene fusions and through comparison with published microarray data. Of 96 genes, 31 were induced and 3 were repressed by Pi starvation in a PhoB dependent manner. Novel Pho regulon members included several genes of unknown function. Comparative analysis across 12 proteobacterial genomes revealed highly conserved Pho regulon members including genes involved in Pi metabolism (pstS, phnC and ppdK). Genes with no obvious association with Pi metabolism were predicted to be Pho regulon members in S.meliloti and multiple organisms. These included smc01605 and smc04317 which are annotated as substrate binding proteins of iron transporters and katA encoding catalase. This data suggests that the Pho regulon overlaps and interacts with several other control circuits, such as the oxidative stress response and iron homeostasis.

Cyclopropane fatty acyl synthase in Sinorhizobium meliloti

“…On: Sat, 12 May 2018 14:12:52 wild-type Pho regulon phenotype and we wished to examine the effects of phosphate limitation on fatty acid cyclopropanation (Yuan et al, 2006b). Accordingly, 263 bp and 271 bp fragments were PCR amplified from within the 59 regions of cfa1 and cfa2, respectively, using primers 59-GCTCTAGAGCTATCGCATATG-ATGAAGTCGTTC-39 (XbaI site in bold) and 59-TGCATGCAT-GTCACAACAGCTTCTGGATCGGATAGG-39 (NsiI site in bold) for cfa1 and primers 59-GCTCTAGAGCGGGATTGTTGAATCTAC-TTCGC-39 (XbaI site in bold) and 59-CCATCGATGGTCACGC-GACGATCGAATTGGTGAAGG-39 (ClaI site in bold) for cfa2.…”

Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021

“…The argE gene is preceded by a potential Pho-box but its expression does not change in response to medium phosphate concentration or phoB inactivation (Yuan et al, 2006). Hippurate hydrolases have been enzymically characterized in a number of bacteria but their physiological role remains undefined (Steele et al, 2006).…”

Bacterial Phosphate Homeostasis: Role of Phosphate Transporters

“…Poly-Pi는 ppk가 생산하는 polyphosphate kinase 에 의해 중합되고, ppx가 생산하는 exopolyphosphatase에 의해 Pi가 한 분자씩 단계적으로 분리된다. ppk와 ppx는 오페론으로 존재하며, 이 오페론은 대부분 PhoB regulon에 속한다 (Yuan et al, 2006). 따라서, PhoB는 세균의 Pi 신호 전달 기능뿐 아니라 세포 내 Pi 대사를 전체적으로 관장하는 조절자라 할 수 있다.…”

“…포도당 대사에 의해 세포 내에 축적되는 glucose-6-P나 alpha-methyl glucoside-6-P 에 의한 포도당-인산 스트레스(glucose-phosphate stress)가 생기 는데, pitA 돌연변이주에서는 간접적으로 PhoB가 활성화되어 PhoB 의존성 alkaline phosphatase가 발현되어 이들을 분해함으 로써, 스트레스를 완화한다 (Richards and Vanderpool, 2012). E. coli의 pst 오페론 중 pstA mRNA 3′ 말단 부위 서열은 rpoS mRNA의 5′ leader 서열과 상호작용하여 RpoS 발현을 증가시킨 다 (Ruiz and Silhavy, 2003;Schurdell et al, 2007) (Kato et al, 1993;AultRiche et al, 1998;Morohoshi et al, 2002;Yuan et al, 2006).…”

“…세균 세포 내부의 Pi 농도는 세포 외부 Pi의 농도가 풍부하거나 결핍되어도 상당히 안정적으 로 유지되고 있는데 (Kuroda et al, 1997;Rao et al, 1998;Yuan et al, 2006) …”