Exploring membrane and cytoplasm proteomic responses of Alkalimonas amylolytica N10 to different external pHs with combination strategy of de novo peptide sequencing

Membrane proteome of the thermoalkaliphile Caldalkalibacillus thermarum TA2.A1

Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound electron transport chain (ETC) enables a great degree of adaptability and is a key part of metabolic adaptation. Knowing what membrane proteins are generally expressed is crucial as a benchmark for further studies. Unfortunately, membrane proteins are the category of proteins hardest to detect using conventional cellular proteomics protocols. In part, this is due to the hydrophobicity of membrane proteins as well as their general lower absolute abundance, which hinders detection. Here, we performed a combination of whole cell lysate proteomics and proteomics of membrane extracts solubilised with either SDS or FOS-choline-12 at various temperatures. The combined methods led to the detection of 158 membrane proteins containing at least a single transmembrane helix (TMH). Within this data set we revealed a full oxidative phosphorylation pathway as well as an alternative NADH dehydrogenase type II (Ndh-2) and a microaerophilic cytochrome oxidase ba3. We also observed C. thermarum TA2.A1 expressing transporters for ectoine and glycine betaine, compounds that are known osmolytes that may assist in maintaining a near neutral internal pH when the external pH is highly alkaline.

Mechanism of TonB-dependent transport system in Halomonas alkalicola CICC 11012s in response to alkaline stress

Halomonas alkalicola CICC 11012s can grow at pH 12.5, the highest pH at which the organisms in the genus Halomonas can grow. Genomic analysis reveals that H. alkalicola adapts to alkaline stress using a variety of adaptive strategies; however, the detailed mechanism for its growth at high-alkaline conditions has not been elucidated. Therefore, in this study, the adaptations of H. alkalicola in response to extreme alkaline stress were investigated. A sharp decrease of alkaliphilic tolerance was observed in mutants E. coli ΔEctonB and H. alkalicola ΔHatonB. Expressions of the gene clusters encoding TonB-dependent transport system and iron complex transport system in H. alkalicola grown under extreme alkaline conditions were markedly up-regulated. We then compared the intracellular ionic iron content and iron-chelating ability of mutant strain with those of wild-type strain to understand the influence of TonB-dependent transport system on the alkaline responses. The results indicated that the presence of TonB-dependent transport system increased the alkaline tolerance of H. alkalicola grown at high-alkaline conditions, but had no effects when the strain was grown at neutral pH and low-alkaline conditions. Meanwhile, the presence of this system increased the transport and accumulation of ionic irons to maintain intracellular metabolic homeostasis, which in turn could increase the tolerance of the strain to extreme alkaline conditions. Based on the results, we established a model representing the interactions between TonB-dependent transport system, alkaline tolerance, and intracellular ionic iron that could help deepen the understanding of the alkaline response mechanism of alkaliphilic bacteria.

Secretome analysis of alkaliphilic bacterium Bacillus lehensis G1 in response to pH changes

Bacillus lehensis G1 is an alkaliphilic bacterium that is capable of surviving in environments up to pH 11. Secretome related to bacterial acclimation in alkaline environment has been less studied compared to cytoplasmic and membrane proteome. The aim of this study was to gain better understanding of bacterial acclimation to alkaline media through analyzing extracellular proteins of B. lehensis. The pH range for B. lehensis growth was conducted, and two-dimensional electrophoresis and MALDI-TOF/TOF MS analysis were conducted to characterize changes in protein profiling in B. lehensis cultured at pH 8 and pH 11 when compared with those cultured at pH 10 (optimal growth pH). B. lehensis could grow well at pH ranging from 8 to 11 in which the bacteria showed to posses thinner flagella at pH 11. Proteomic analyses demonstrated that five proteins were up-regulated and 13 proteins were down-regulated at pH 8, whereas at pH 11, 14 proteins were up-regulated and 8 were down-regulated. Majority of the differentially expressed proteins were involved in the cell wall, main glycolytic pathways, the metabolism of amino acids and related molecules and some proteins of unknown function. A total of 40 differentially expressed protein spots corresponding to 33 proteins were identified; including GlcNAc-binding protein A, chitinase, endopeptidase lytE, flagellar hook-associated proteins and enolase. These proteins may play important roles in acclimation to alkaline media via reallocation of cell wall structure and changes to cell surface glycolytic enzymes, amino acid metabolism, flagellar hook-associated proteins and chaperones to sustain life under pH-stressed conditions.

Overexpression of AaPal, a peptidoglycan-associated lipoprotein from Alkalomonas amylolytica, improves salt and alkaline tolerance of Escherichia coli and Arabidopsis thaliana

The outer membrane lipoprotein, Pal, plays a major role maintaining the integrity of outer membrane and cell morphology in Gram-negative bacteria. Here, we represent A novel role of AaPal in tolerance to salt and alkaline stresses. The cell density of Escherichia coli expressing AaPal was approx. three times as that of control strain when grown in the presence of 1 M NaCl or at pH 9.0 for 14 h, and transgenic Arabidopsis thaliana grew taller and stronger than wild-type plants when subjected to 200 mM NaCl or pH 9.0 stress. This tolerance was attributed to higher concentrations of K(+) and lower concentrations of Na(+) in the transgenic organism. Our study provides a potential use of AaPal in the improvement of salt and alkaline tolerance in bacteria and plants.

An on-target desalting and concentration sample preparation protocol for MALDI-MS and MS/MS analysis

2DE coupled with MALDI-MS is one of the most widely used and powerful analytic technologies in proteomics study. The MALDI sample preparation method has been developed and optimized towards the combination of simplicity, sample-cleaning, and sample concentration since its introduction. Here we present a protocol of the so-called Sample loading, Matrix loading, and on-target Wash (SMW) method which fulfills the three criteria by taking advantage of the AnchorChip™ targets. Our method is extremely simple and no pre-desalting or concentration is needed when dealing with samples prepared from 2DE. The protocol is amendable for automation and would pave the road for high-throughput MALDI-MS or MS/MS-based proteomics studies with guaranteed sensitivity and high identification rate. The method has been successfully applied to mouse liver proteome study and so far has been employed in other proteome studies by world-wide researchers.