Collaborators. Simon Levin Princeton University. James Elser Arizona State University

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1 Collaborators Simon Levin Princeton University James Elser Arizona State University

2 Patterns in molecules and oceans: linking cellular machinery to global N:P ratios Irakli Loladze Department of Mathematics University of Nebraska - Lincoln February 4, 2006

3 Nitrogen, N Phosphorus, P N:P

4 N:P in Oceanic Water and Phytoplankton

5 What is the motivation? N and P are essential to all life and globally limit plant and phytoplankton growth Phytoplankton plays key roles in climate regulation and biogeochemical cycles

6 Redfield Ratios Alfred C. Redfield (1958): "The Biological Control of Chemical Factors in the Environment.

7 Redfield Ratios Alfred C. Redfield (1958): "The Biological Control of Chemical Factors in the Environment. Water N:P = Plankton N:P =16

8 Is this generally true? Is Organismal Stoichiometry = Environmental Stoichiometry? IN: Atmosphere? Lakes? Soil?

9 NO, NO, NO Oceans are kind of special

10 Water N:P = Plankton N:P = 16

11 Water N:P = Plankton N:P = 16 A Million dollar Questions: 1) Why =?

12 Water N:P = Plankton N:P = 16 A Million dollar Questions: 1) Why = in Oceans? 2) Why 16?

13 Revisiting Redfield Water N:P = Plankton N:P =16?

14 Revisiting Redfield Water N:P = Plankton N:P =16?

15 Revisiting Redfield Water N:P = Plankton N:P =16?

16 Not a pretty picture In oceanic water: Near Bermuda N:P = 30-35, but near Hawaii N:P = 1-5 In phytoplankton species N:P range is at least Is Redfield true at all, where is 16?

17 Wu et al (2000) Science, v.289

18 In Deep Ocean N:P = 16! Wu et al (2000) Science, v.289

19 Yes, many species of phytoplankton, but the Average Phytoplankton N:P ~16

20 Ocean 16 Surface zone Average Phytoplankton N:P ~16 Thermocline Deep zone Deep Water N:P = 16

21 1. Why =? Average Phytoplankton N:P = Deep Ocean Water N:P?

22 Ecological Stoichiometry The study of the balance of energy and multiple chemical elements in ecological systems The first picture of a ribosome. Cate et al. (1999) Science 285:

28 A couple of Stoichiometric Principles: Life cannot create, destroy or convert any chemical element C,H,O,N, and P are essential to all Life

29 How many biological systems can be COMPLETELY described by these principles?

30 NONE

31 For how many biological systems these principles are true?

32 All

33 1. Why =? Average Phytoplankton N:P = Deep Ocean Water N:P?

34 Because of Rat in a box

35 After 500 years Stoichiometry = Stoichiometry

36 Ocean Average Phytoplankton N:P ~16 Thermocline Deep Water N:P = 16 = because It Sinks!

37 2)Why 16? Average Phytoplankton N:P = Deep Ocean Water N:P = 16 Why not 3, 8, 25, 53, 700?

38 Phytoplankton s demand for N and P N and P for nucleotides (RNA & DNA) N for Proteins

39 Protein Synthesis Machinery Translation

40 RNA Protein Translation P N

41 = N % in Proteins, ~17% RNA Protein Translation P N

42 RNA Protein Transcription P N

43 Elemental Composition of Nucleotides Adenine: C5H5N5 Guanine: C5H5N5O Cytosine: C4H5N3O Thymine: C5H6N2O2 Uracil (in RNA replaces Thymine) C4H4N2O2 Phosphate: PO4 2-deoxyribose: C5H9O4 (using one can get % of each elements (e.g. for adenine: C5H5N5PO4C5H9O4) Adenine C ; H 3.885; N ; O ; P 8.527; Guanine C ; H 3.721; N ; O ; P 8.167; Cytosine C ; H 4.160; N ; O ; P 9.131; Thymine C ; H 3.995; N 7.931; O ; P 8.769; Uracil C ; H 3.851; N 8.234; O ; P 9.105; RNA is : 8.7% P, 14.6% N

44 = P % in RNA, ~8.7% = N % in RNA, ~14.6% RNA Protein Transcription P N

45 = P % in RNA, ~14.6% = N % in RNA, ~14.6% = N % in Proteins, ~17% RNA Protein Transcription Translation P N

46 What is biochemically optimal Protein:RNA =?

47 Entire Cell = RNA + Protein Protein:RNA = Protein concentration in a cell = RNA concentration in a cell = N:P of a cell = = 16?

48 Entire Cell = RNA + Protein Protein:RNA = Protein concentration in a cell = RNA concentration in a cell = N:P of a cell = =?

54 = P % in RNA, ~14.6% = N % in RNA, ~14.6% = N % in Proteins, ~17% RNA Protein Transcription Translation P N

55 Optimal Protein:RNA = Optimal = $% l s N:P of a cell =

56 Biochemically optimal N:P ratio arises from five fundamental constants of life:

57 With data from Bremer & Dennis Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate, one gets N:P = Optimal N:P RNA Polymerase / Total Protein, f pl

58 A PROBLEM. CELL Ocean

59 Adding Evolution If species with various RNA:Protein compete, who wins?

60 dn dt dp dt dn s dt dp s = n u( n) x n 0 = p u( p) x p n p 0 1 ( ) (1 ) ( ns, s, ) 1 ( ) ( ns, s, ) 1 x= (1 + ) r is RNA:Protein ratio n p Model = un x + f p r n = u p x f p r p dt dr = n f( ns, ps, r) r dt f( n, p, r) = min r, min{, } x { n n p } s s s s s s s

61 Equilibrium dependence on RNA:Protein, but it also depends on incoming N:P

62 Result Evolutionary winner s N:P depends on the incoming N:P

63 Result Evolutionary winner s N:P depends on the incoming N:P Is this irrelevant?? Not good.

64 Ocean 16 Surface zone Average Phytoplankton N:P ~16 Thermocline Deep zone Deep Water N:P = 16

65 Result! Once the winner s N:P is fed back into the incoming N:P, it converges to biochemically optimal N:P!

66 P N

67 THANK YOU for Listening!

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis

Chapters 12&13 Notes: DNA, RNA & Protein Synthesis Name Period Words to Know: nucleotides, DNA, complementary base pairing, replication, genes, proteins, mrna, rrna, trna, transcription, translation, codon,