Biology subjects

Saier, M. H.

Publications and source records attributed to Saier, M. H..

6 recordsLinked to original sources

bioRxiv2021

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YgfI, YiaU, YneJ, YcaN, YbhD. We show that: 1) YbdO regulation has an effect on bacterial growth at low pH with citrate supplementation. YbdO is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); 2) YgfI activates the dhaKLM operon that encodes the phosphotransferase system involved in glycerol and dihydroxyacetone utilization; 3) YiaU regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase; 4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of L-glutamate and putrescine as nitrogen sources; and 5) YbhD and YcaN regulate adjacent y-genes on the genome and YbeF is involved in flagella gene regulation. We have thus established the functions for four LTFs and identified the target genes for three LTFs. IMPORTANCEThe reconstruction of the transcriptional regulatory network (TRN) is important for gram-negative bacteria such as E. coli. LysR-type TFs are abundant in Enterobacteria, but many LTF functions still remain unknown. Here we report putative functions of uncharacterized TFs based on multi-omics data related to L-threonine, L-glutamate, and putrescine utilization. Amino acids (AAs) and polyamines are important sources of nitrogen for many microorganisms, but the increase in one amino acid or putrescine concentration in a minimal medium also induces stress. Although polyamine metabolism has been studied, the TRN that controls the putrescine (Ptr) and AA utilization at minimal medium conditions are still poorly understood. The function of previously uncharacterized transcriptional regulators YbdO, YgfI, and YneJ (PtrR) were identified in Escherichia coli. PtrR is important for Ptr and L-glutamate utilization, while YgfI transcriptional regulation was found to be important for growth on L-threonine and glycerol as a carbon source.

systems biology↗

bioRxiv2020

PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization

Although polyamines, such as putrescine (Ptr), induce envelope stress for bacteria, they are important as nitrogen and carbon sources. Ptr utilization in Escherichia coli involves protein glutamylation, and glutamate stands at a crossroads between catabolism and anabolism. This communication reports that the transcription factor YneJ, here renamed PtrR, is involved in the regulation of a small regulatory RNA gene, fnrS, and an operon, yneIHGF, encoding succinate-semialdehyde dehydrogenase, Sad (YneI), glutaminase, GlsB (YneH), and several other genes. The yneI promoter is activated during putrescine utilization under nitrogen/carbon starvation conditions, and we show that PtrR is important for the putrescine stress response. It is also a repressor of fnrS gene expression, involved in the cascade regulation of mRNA synthesis for the marA and sodB genes, involved in antibiotic responses. PtrR transcriptional regulation of fnrS leads to a regulatory cascade induced by this small RNA that affects mRNA levels of ompF and the multidrug resistance regulator, MarA. We propose that PtrR functions as a dual activator/repressor, and that its regulation is important for the responses to different stress conditions involving L-glutamine/L-glutamate and putrescine utilization. IMPORTANCEPutrescine is an important source of nitrogen for many organisms, but it also induces stress. Although its metabolism has been studied extensively, the regulatory mechanisms that control the stress response are still poorly understood. This study reveals that the HTH-type transcriptional regulator, YneJ in Escherichia coli, here re-named PtrR, is important for the putrescine stress response, in part because it plays a role in outer membrane porin regulation as a sensor in a regulatory cascade. Direct PtrR transcriptional regulation of the fnrS, yneI (sad), gltS and ptrR genes is documented and rationalized, and nine PtrR binding sites were identified using ChIP-Exo. A ptrR mutant exhibited altered resistance to a tetracycline group of antibiotics under microaerophilic conditions, suggesting that PtrR indirectly controls expression of porin genes such as ompF.

microbiology↗

bioRxiv2020

UDP-glucose dehydrogenase Ugd in E. coli is activated by Gmd and RffD, is inhibited by CheY, and regulates swarming

The two most common mechanisms of polymyxin resistance in bacteria involve glycosylation of the outer membrane lipopolysaccharide (LPS) and production of the exocapsular polysaccharide, colanic acid (CA). UDP-glucose dehydrogenase, Ugd, is required for both CA biosynthesis and LPS modification. We here show that Ugd is activated by the GDP-mannose-4,6-dehydratase (Gmd, YefA, YefN), UDP-N-acetyl-D-mannosamine dehydrogenase (RffD, WecC), and ribonuclease HII (RnhB). The former two enzymes are involved in Lipid A and colanic acid biosyntheses, respectively, while RnhB cleaves RNA in RNA:DNA hybrids. Moreover, CheY inhibits the phosphorylated, activated form of Ugd (Ugd-P). Finally, Ugd is involved in the regulation of swarming, since a ugd mutant has an increased swarming rate, while Ugd overproduction inhibits swarming. Two-hybrid bacterial assays reveal direct interaction of Ugd with RssB (an anti-RpoS factor) and CheY in vivo.

biochemistry↗

bioRxiv2019

Reclassification of SLC22 Transporters: Analysis of OAT, OCT, OCTN, and other Family Members Reveals 8 Functional Subgroups

Among transporters, the SLC22 family is emerging as a central hub of endogenous physiology. The family consists of organic anion transporters (OATs), organic cation transporters (OCTs) and zwitterion transporters (OCTNs). Despite being known as "drug" transporters, these multi-specific, oligo-specific, and relatively mono-specific transporters facilitate the movement of metabolites and key signaling molecules. An in-depth reanalysis supports a reassignment of these proteins into eight functional subgroups with four new subgroups arising from the previously defined OAT subclade. These OAT subgroups are: OATS1 (SLC22A6, SLC22A8, and SLC22A20), OATS2 (SLC22A7), OATS3 (SLC22A11, SLC22A12, and Slc22a22), and OATS4 (SLC22A9, SLC22A10, SLC22A24, and SLC22A25). We propose merging the OCTN (SLC22A4, SLC22A5, and Slc22a21) and OCT-related (SLC22A15 and SLC22A16) subclades into the OCTN/OCTN-related subgroup. Functional support for the eight subgroups comes from network analysis of data from GWAS, in vivo models, and in vitro assays. These data emphasize shared substrate specificity of SLC22 transporters for characteristic metabolites such as prostaglandins, uric acid, carnitine, creatinine, and estrone sulfate. Some important subgroup associations include: OATS1 with metabolites, signaling molecules, uremic toxins and odorants, OATS2 with cyclic nucleotides, OATS3 with uric acid, OATS4 with conjugated sex hormones, particularly etiocholanolone glucuronide, OCT with monoamine neurotransmitters, and OCTN/OCTN-related with ergothioneine and carnitine derivatives. The OAT-like and OAT-related subgroups remain understudied and therefore do not have assigned functionality. Relatedness within subgroups is supported by multiple sequence alignments, evolutionarily conserved protein motifs, genomic localization, and tissue expression. We also highlight low level sequence similarity of SLC22 members with other non-transport proteins. Our data suggest that the SLC22 family can work among itself, as well as with other transporters and enzymes, to optimize levels of numerous metabolites and signaling molecules, as proposed by the Remote Sensing and Signaling Theory.

pharmacology and toxicology↗

bioRxiv2019

Protein:Protein Interactions in the Cytoplasmic Membrane Influencing Sugar Transport and Phosphorylation Activities of the E. coli Phosphotransferase System.

The multicomponent phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system (PTS) in Escherichia coli takes up sugar substrates and concomitantly phosphorylates them. We have recently provided evidence that many of the integral membrane PTS permeases interact with the fructose PTS (FruA/FruB) [1]. However, the biochemical and physiological significance of this finding was not known. We have carried out molecular genetic/biochemical/physiological studies that show that interactions of the fructose PTS often enhance, but sometimes inhibit the activities of other PTS transporters many fold, depending on the target PTS system under study. Thus, the glucose, mannose, mannitol and N- acetylglucosamine permeases exhibit enhanced in vivo sugar transport and sometimes in vitro PEP-dependent sugar phosphorylation activities while the galactitol and trehalose systems show inhibited activities. This is observed when the fructose system is induced to high levels and prevented when the fruA/fruB genes are deleted. Overexpression of the fruA and/or fruB genes in the absence of fructose induction during growth also enhances the rates of uptake of other hexoses. The {beta}-galactosidase activities of man, mtl, and gat-lacZ transcriptional fusions and the sugar-specific transphosphorylation activities of these enzyme transporters were not affected either by frustose induction or fruAB overexpression, showing that the rates of synthesis and protein levels in the membrane of the target PTS permeases were not altered. We thus suggest that specific protein-protein interactions within the cytoplasmic membrane regulate transport in vivo (and sometimes the PEP-dependent phosphorylation activities in vitro of PTS permeases) in a physiologically meaningful way that may help to provide a hierarchy of preferred PTS sugars. These observations appear to be applicable in principle to other types of transport systems as well.

microbiology↗

bioRxiv2018

Cryo-EM Structure of OSCA1.2 from Oryza sativa: Mechanical basis of hyperosmolality-gating in Plants

Sensing and responding to environmental water deficiency and osmotic stresses is essential for the growth, development and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality in Arabidopsis. Here, we report the cryo-EM structure and function of an ion channel from rice (Oryza sativa; OsOSCA1.2), showing how it mediates hyperosmolality sensing and ion permeability. The structure reveals a dimer; the molecular architecture of each subunit consists of eleven transmembrane helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The transmembrane domain is structurally related to the TMEM16 family of calcium dependent ion channels and scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that is parallel to the plasma membrane. These helical arms are well positioned to sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the transmembrane portion of the molecule to open the channel. Hydrogen-deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. The structure provides a framework to understand the structural basis of hyperosmolality sensing in an important crop plant, extends our knowledge of the anoctamin superfamily important for plants and fungi, and provides a structural mechanism for translating membrane stress to ion transport regulation.

biophysics↗